Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6318584.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6318584.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6318584.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.17, per 1000 atoms: 0.35 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 115.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 708 0.94 - 1.20: 988 1.20 - 1.47: 751 1.47 - 1.73: 691 1.73 - 1.99: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.236 0.983 0.254 1.15e-02 7.56e+03 4.88e+02 bond pdb=" C MET A 134 " pdb=" O MET A 134 " ideal model delta sigma weight residual 1.235 0.961 0.274 1.33e-02 5.65e+03 4.26e+02 bond pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 1.236 1.432 -0.196 1.01e-02 9.80e+03 3.78e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.525 1.273 0.252 1.32e-02 5.74e+03 3.64e+02 bond pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 1.334 1.569 -0.234 1.27e-02 6.20e+03 3.40e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 3191 4.89 - 9.78: 1922 9.78 - 14.67: 560 14.67 - 19.56: 96 19.56 - 24.46: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 138.68 -16.56 1.06e+00 8.90e-01 2.44e+02 angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 107.91 14.27 9.60e-01 1.09e+00 2.21e+02 angle pdb=" O BGLN A 80 " pdb=" C BGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 122.12 137.79 -15.67 1.06e+00 8.90e-01 2.18e+02 angle pdb=" O BPRO A 66 " pdb=" C BPRO A 66 " pdb=" N BTYR A 67 " ideal model delta sigma weight residual 121.10 145.56 -24.46 1.90e+00 2.77e-01 1.66e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.55 108.59 11.96 9.50e-01 1.11e+00 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1317 17.96 - 35.93: 118 35.93 - 53.89: 30 53.89 - 71.85: 14 71.85 - 89.81: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -143.49 20.89 0 2.50e+00 1.60e-01 6.98e+01 dihedral pdb=" C LEU A 77 " pdb=" N LEU A 77 " pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta harmonic sigma weight residual -122.60 -140.98 18.38 0 2.50e+00 1.60e-01 5.41e+01 dihedral pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual 122.80 140.26 -17.46 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.213: 86 0.213 - 0.425: 82 0.425 - 0.637: 48 0.637 - 0.849: 21 0.849 - 1.061: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.46 1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CA ALA A 171 " pdb=" N ALA A 171 " pdb=" C ALA A 171 " pdb=" CB ALA A 171 " both_signs ideal model delta sigma weight residual False 2.48 1.49 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA THR A 19 " pdb=" N THR A 19 " pdb=" C THR A 19 " pdb=" CB THR A 19 " both_signs ideal model delta sigma weight residual False 2.53 3.50 -0.97 2.00e-01 2.50e+01 2.36e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.129 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG TYR A 141 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.096 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.004 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG BTYR A 67 " -0.070 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.110 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.106 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.039 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.022 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.061 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.017 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" CG PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.065 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.080 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 785 2.28 - 2.86: 7830 2.86 - 3.44: 10690 3.44 - 4.02: 15318 4.02 - 4.60: 21984 Nonbonded interactions: 56607 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.699 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.825 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.837 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.850 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.854 2.450 ... (remaining 56602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_6318584_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3617 r_free= 0.2028 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465722 | | target function (ml) not normalized (work): 22016.010403 | | target function (ml) not normalized (free): 1146.670690 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3800 0.2254 4.8471 4.903| | 2: 3.78 - 3.00 1.00 2430 110 0.3393 0.1646 4.0733 4.095| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.70 0.83 0.13 6593.30| | 2: 3.78 - 3.00 2430 110 0.94 11.36 1.48 0.26 449.06| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 385.33 max = 12056.61 mean = 3564.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.30| |phase err.(test): min = 0.00 max = 89.95 mean = 33.32| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.274 1557 Z= 5.356 Angle : 5.348 24.455 2118 Z= 3.727 Chirality : 0.406 1.061 243 Planarity : 0.030 0.124 284 Dihedral : 14.099 89.814 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.47), residues: 224 helix: -2.38 (0.39), residues: 108 sheet: -0.28 (0.83), residues: 30 loop : -0.84 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.019 ARG A 27 TYR 0.102 0.042 TYR A 141 PHE 0.098 0.032 PHE A 119 HIS 0.041 0.022 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3617 r_free= 0.2028 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465722 | | target function (ml) not normalized (work): 22016.010403 | | target function (ml) not normalized (free): 1146.670690 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3573 0.3649 0.2124 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3573 0.3649 0.2124 n_refl.: 5182 remove outliers: r(all,work,free)=0.2512 0.2535 0.2124 n_refl.: 5178 overall B=-2.51 to atoms: r(all,work,free)=0.2416 0.2436 0.2083 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1566 0.1565 0.1596 n_refl.: 5178 remove outliers: r(all,work,free)=0.1564 0.1563 0.1596 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4035 444.937 409.825 0.628 1.082 0.394 11.894-9.307 99.02 97 4 0.1884 714.291 689.824 0.894 1.077 0.377 9.237-7.194 100.00 213 7 0.2169 584.149 575.991 0.927 1.069 0.353 7.162-5.571 100.00 427 22 0.2328 438.333 421.811 0.890 1.053 0.288 5.546-4.326 100.00 867 58 0.1389 601.768 593.575 0.947 1.029 0.220 4.315-3.360 100.00 1859 96 0.1303 572.288 566.378 1.028 0.987 0.199 3.356-3.002 100.00 1373 60 0.1609 440.801 433.437 1.052 0.946 0.096 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.3678 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1563 r_free=0.1596 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1563 r_free=0.1597 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.485910 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.821986 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1162 0.1789 0.0626 0.010 1.0 1.9 0.5 0.0 0 9.743 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 17.89 6.26 3.013 16.352 1.822 0.018 10.18 17.83 7.65 5.011 16.590 1.822 0.015 Individual atomic B min max mean iso aniso Overall: 2.58 111.86 17.83 5.36 1785 0 Protein: 2.58 111.86 15.13 5.35 1519 0 Water: 4.36 111.79 33.53 N/A 258 0 Other: 16.85 35.66 24.46 N/A 8 0 Chain A: 2.58 111.86 17.83 N/A 1785 0 Histogram: Values Number of atoms 2.58 - 13.51 919 13.51 - 24.44 479 24.44 - 35.37 192 35.37 - 46.30 106 46.30 - 57.22 56 57.22 - 68.15 16 68.15 - 79.08 8 79.08 - 90.01 5 90.01 - 100.94 1 100.94 - 111.86 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1783 r_work=0.1011 r_free=0.1787 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1011 r_free = 0.1787 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1015 r_free = 0.1774 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1015 r_free= 0.1774 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014057 | | target function (ls_wunit_k1) not normalized (work): 69.230988 | | target function (ls_wunit_k1) not normalized (free): 10.410451 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1054 0.1015 0.1774 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2115 0.2114 0.2240 n_refl.: 5177 remove outliers: r(all,work,free)=0.2115 0.2114 0.2240 n_refl.: 5177 overall B=-0.94 to atoms: r(all,work,free)=0.2074 0.2072 0.2230 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1019 0.1782 n_refl.: 5177 remove outliers: r(all,work,free)=0.1056 0.1017 0.1782 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3402 312.835 297.727 0.619 1.027 0.365 11.894-9.307 99.02 97 4 0.1501 506.541 499.453 0.934 1.026 0.361 9.237-7.194 100.00 213 7 0.1707 414.250 412.983 0.976 1.024 0.331 7.162-5.571 100.00 427 22 0.1629 310.844 307.950 0.936 1.018 0.292 5.546-4.326 100.00 867 58 0.0913 426.745 424.160 0.962 1.010 0.205 4.315-3.360 100.00 1859 96 0.0767 405.839 405.773 1.019 0.996 0.200 3.356-3.002 100.00 1373 60 0.1004 312.594 311.104 1.006 0.982 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.2214 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1782 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1017 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1782 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1051 r_free=0.1796 | n_water=247 | time (s): 20.660 (total time: 21.330) Filter (q & B) r_work=0.1051 r_free=0.1796 | n_water=244 | time (s): 1.500 (total time: 22.830) Compute maps r_work=0.1051 r_free=0.1796 | n_water=244 | time (s): 0.590 (total time: 23.420) Filter (map) r_work=0.1329 r_free=0.1918 | n_water=148 | time (s): 1.380 (total time: 24.800) Find peaks r_work=0.1329 r_free=0.1918 | n_water=148 | time (s): 0.520 (total time: 25.320) Add new water r_work=0.1673 r_free=0.2172 | n_water=232 | time (s): 1.620 (total time: 26.940) Refine new water occ: r_work=0.1166 r_free=0.1697 adp: r_work=0.1141 r_free=0.1698 occ: r_work=0.1140 r_free=0.1684 adp: r_work=0.1127 r_free=0.1693 occ: r_work=0.1126 r_free=0.1684 adp: r_work=0.1123 r_free=0.1687 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1687 r_work=0.1123 r_free=0.1687 | n_water=232 | time (s): 3.790 (total time: 30.730) Filter (q & B) r_work=0.1123 r_free=0.1687 | n_water=232 | time (s): 0.900 (total time: 31.630) Filter (dist only) r_work=0.1129 r_free=0.1690 | n_water=229 | time (s): 17.650 (total time: 49.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.033121 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.627669 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1016 0.1832 0.0816 0.010 1.0 3.2 0.5 0.6 0 12.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.16 18.32 8.16 4.736 17.266 2.628 0.014 9.50 18.66 9.17 5.516 17.655 2.628 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.92 17.03 6.52 1756 0 Protein: 0.00 106.92 15.47 6.52 1519 0 Water: 0.00 63.13 27.20 N/A 229 0 Other: 11.88 30.49 21.41 N/A 8 0 Chain A: 0.00 106.92 16.20 N/A 1673 0 Chain S: 0.00 57.93 33.85 N/A 83 0 Histogram: Values Number of atoms 0.00 - 10.69 626 10.69 - 21.38 710 21.38 - 32.08 216 32.08 - 42.77 114 42.77 - 53.46 47 53.46 - 64.15 29 64.15 - 74.84 7 74.84 - 85.54 2 85.54 - 96.23 3 96.23 - 106.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.0950 r_free=0.1866 r_work=0.0946 r_free=0.1867 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0946 r_free = 0.1867 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0939 r_free = 0.1864 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0939 r_free= 0.1864 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.012046 | | target function (ls_wunit_k1) not normalized (work): 59.312407 | | target function (ls_wunit_k1) not normalized (free): 10.360163 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0987 0.0939 0.1864 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2152 0.2154 0.2242 n_refl.: 5176 remove outliers: r(all,work,free)=0.2152 0.2154 0.2242 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2152 0.2154 0.2242 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0988 0.0940 0.1875 n_refl.: 5176 remove outliers: r(all,work,free)=0.0988 0.0940 0.1875 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3470 312.835 296.799 0.621 1.009 0.354 11.894-9.307 99.02 97 4 0.1407 506.541 500.053 0.950 1.010 0.350 9.237-7.194 100.00 213 7 0.1480 414.250 413.320 0.991 1.010 0.304 7.162-5.571 100.00 427 22 0.1429 310.844 307.700 0.961 1.008 0.290 5.546-4.326 100.00 867 58 0.0800 426.745 423.927 0.981 1.005 0.230 4.315-3.360 100.00 1859 96 0.0725 405.839 405.764 1.034 0.999 0.200 3.356-3.002 100.00 1373 60 0.0960 312.594 312.595 1.021 0.993 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.3168 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0940 r_free=0.1875 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0941 r_free=0.1879 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0941 r_free=0.1879 | n_water=229 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.0963 r_free=0.1914 | n_water=223 | time (s): 17.280 (total time: 17.930) Filter (q & B) r_work=0.1023 r_free=0.1899 | n_water=220 | time (s): 1.290 (total time: 19.220) Compute maps r_work=0.1023 r_free=0.1899 | n_water=220 | time (s): 0.490 (total time: 19.710) Filter (map) r_work=0.1260 r_free=0.1932 | n_water=152 | time (s): 1.350 (total time: 21.060) Find peaks r_work=0.1260 r_free=0.1932 | n_water=152 | time (s): 0.490 (total time: 21.550) Add new water r_work=0.1614 r_free=0.2239 | n_water=233 | time (s): 1.490 (total time: 23.040) Refine new water occ: r_work=0.1062 r_free=0.1822 adp: r_work=0.1058 r_free=0.1846 occ: r_work=0.1047 r_free=0.1831 adp: r_work=0.1047 r_free=0.1836 occ: r_work=0.1038 r_free=0.1825 adp: r_work=0.1038 r_free=0.1831 ADP+occupancy (water only), MIN, final r_work=0.1038 r_free=0.1831 r_work=0.1038 r_free=0.1831 | n_water=233 | time (s): 11.950 (total time: 34.990) Filter (q & B) r_work=0.1039 r_free=0.1836 | n_water=231 | time (s): 2.000 (total time: 36.990) Filter (dist only) r_work=0.1052 r_free=0.1830 | n_water=228 | time (s): 17.220 (total time: 54.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.109065 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.248337 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0945 0.1884 0.0938 0.011 1.1 4.2 0.5 0.0 0 0.555 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.45 18.84 9.38 5.457 18.206 0.248 5.132 9.01 18.78 9.76 7.248 18.234 0.248 5.036 Individual atomic B min max mean iso aniso Overall: 0.00 106.01 16.78 8.94 1755 0 Protein: 0.00 106.01 15.66 8.94 1519 0 Water: 0.00 58.13 24.07 N/A 228 0 Other: 9.71 34.90 21.71 N/A 8 0 Chain A: 0.00 106.01 16.24 N/A 1655 0 Chain S: 0.00 55.87 25.70 N/A 100 0 Histogram: Values Number of atoms 0.00 - 10.60 619 10.60 - 21.20 704 21.20 - 31.80 231 31.80 - 42.40 126 42.40 - 53.00 37 53.00 - 63.60 20 63.60 - 74.21 11 74.21 - 84.81 2 84.81 - 95.41 3 95.41 - 106.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1878 r_work=0.0906 r_free=0.1884 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0906 r_free = 0.1884 target_work(ml) = 5.040 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0893 r_free = 0.1866 target_work(ml) = 5.031 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0893 r_free= 0.1866 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.031442 | | target function (ml) not normalized (work): 24774.822850 | | target function (ml) not normalized (free): 1850.543964 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0942 0.0893 0.1866 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2172 0.2178 0.2221 n_refl.: 5176 remove outliers: r(all,work,free)=0.2172 0.2178 0.2221 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2172 0.2178 0.2221 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0889 0.1863 n_refl.: 5176 remove outliers: r(all,work,free)=0.0935 0.0887 0.1863 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3833 314.879 282.667 0.566 0.996 0.328 11.894-9.307 99.02 97 4 0.1773 506.541 494.137 0.956 1.000 0.327 9.237-7.194 100.00 213 7 0.1868 414.250 408.350 1.013 1.001 0.310 7.162-5.571 100.00 427 22 0.1789 310.844 303.919 0.988 1.001 0.290 5.546-4.326 100.00 867 58 0.0922 426.745 421.972 1.008 1.001 0.230 4.315-3.360 100.00 1859 96 0.0586 405.839 405.208 1.068 1.002 0.210 3.356-3.002 100.00 1373 60 0.0614 312.594 312.142 1.050 1.001 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9172 b_overall=-7.0041 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0887 r_free=0.1863 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0887 r_free=0.1863 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0887 r_free=0.1863 | n_water=228 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0905 r_free=0.1867 | n_water=221 | time (s): 19.100 (total time: 19.680) Filter (q & B) r_work=0.0954 r_free=0.1879 | n_water=219 | time (s): 1.440 (total time: 21.120) Compute maps r_work=0.0954 r_free=0.1879 | n_water=219 | time (s): 0.420 (total time: 21.540) Filter (map) r_work=0.1224 r_free=0.1893 | n_water=152 | time (s): 1.250 (total time: 22.790) Find peaks r_work=0.1224 r_free=0.1893 | n_water=152 | time (s): 0.400 (total time: 23.190) Add new water r_work=0.1542 r_free=0.2213 | n_water=224 | time (s): 1.410 (total time: 24.600) Refine new water occ: r_work=0.1029 r_free=0.1868 adp: r_work=0.1024 r_free=0.1880 occ: r_work=0.1015 r_free=0.1862 adp: r_work=0.1015 r_free=0.1869 occ: r_work=0.1006 r_free=0.1850 adp: r_work=0.1006 r_free=0.1856 ADP+occupancy (water only), MIN, final r_work=0.1006 r_free=0.1856 r_work=0.1006 r_free=0.1856 | n_water=224 | time (s): 12.360 (total time: 36.960) Filter (q & B) r_work=0.1007 r_free=0.1857 | n_water=223 | time (s): 1.920 (total time: 38.880) Filter (dist only) r_work=0.1008 r_free=0.1851 | n_water=221 | time (s): 17.880 (total time: 56.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.017550 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.240697 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0915 0.1830 0.0915 0.011 1.1 6.4 0.5 0.6 0 0.509 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.15 18.30 9.15 6.986 18.372 0.241 5.025 8.87 18.54 9.66 8.410 18.445 0.241 4.955 Individual atomic B min max mean iso aniso Overall: 0.00 105.36 16.93 10.91 1748 0 Protein: 0.00 105.36 16.01 10.90 1519 0 Water: 0.00 58.36 23.15 N/A 221 0 Other: 8.36 36.71 20.60 N/A 8 0 Chain A: 0.00 105.36 16.43 N/A 1641 0 Chain S: 0.00 58.23 24.65 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.54 607 10.54 - 21.07 669 21.07 - 31.61 275 31.61 - 42.14 106 42.14 - 52.68 51 52.68 - 63.22 19 63.22 - 73.75 11 73.75 - 84.29 5 84.29 - 94.82 1 94.82 - 105.36 4 =========================== Idealize ADP of riding H ========================== r_work=0.0887 r_free=0.1854 r_work=0.0893 r_free=0.1859 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1859 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1835 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1835 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.952727 | | target function (ml) not normalized (work): 24382.272704 | | target function (ml) not normalized (free): 2033.269036 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0929 0.0881 0.1835 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2148 0.2149 0.2232 n_refl.: 5175 remove outliers: r(all,work,free)=0.2148 0.2149 0.2232 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2148 0.2149 0.2232 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0880 0.1835 n_refl.: 5175 remove outliers: r(all,work,free)=0.0927 0.0880 0.1835 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3872 314.879 289.166 0.573 0.989 0.319 11.894-9.307 99.02 97 4 0.1922 506.541 491.689 0.952 0.994 0.319 9.237-7.194 100.00 213 7 0.2017 414.250 404.206 1.022 0.996 0.310 7.162-5.571 100.00 427 22 0.1937 310.844 301.512 0.999 0.998 0.300 5.546-4.326 100.00 867 58 0.0980 426.745 421.252 1.017 1.000 0.230 4.315-3.360 100.00 1859 96 0.0568 405.839 405.337 1.086 1.002 0.220 3.356-3.002 100.00 1373 60 0.0472 312.594 312.871 1.072 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9179 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0880 r_free=0.1835 After: r_work=0.0883 r_free=0.1835 ================================== NQH flips ================================== r_work=0.0883 r_free=0.1835 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0883 r_free=0.1832 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1832 | n_water=221 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0907 r_free=0.1845 | n_water=216 | time (s): 17.680 (total time: 18.190) Filter (q & B) r_work=0.1046 r_free=0.1874 | n_water=212 | time (s): 1.260 (total time: 19.450) Compute maps r_work=0.1046 r_free=0.1874 | n_water=212 | time (s): 0.530 (total time: 19.980) Filter (map) r_work=0.1274 r_free=0.1982 | n_water=153 | time (s): 1.740 (total time: 21.720) Find peaks r_work=0.1274 r_free=0.1982 | n_water=153 | time (s): 0.590 (total time: 22.310) Add new water r_work=0.1561 r_free=0.2169 | n_water=222 | time (s): 1.720 (total time: 24.030) Refine new water occ: r_work=0.1007 r_free=0.1837 adp: r_work=0.0994 r_free=0.1845 occ: r_work=0.0986 r_free=0.1831 adp: r_work=0.0985 r_free=0.1837 occ: r_work=0.0977 r_free=0.1824 adp: r_work=0.0976 r_free=0.1829 ADP+occupancy (water only), MIN, final r_work=0.0976 r_free=0.1829 r_work=0.0976 r_free=0.1829 | n_water=222 | time (s): 11.710 (total time: 35.740) Filter (q & B) r_work=0.0976 r_free=0.1829 | n_water=222 | time (s): 0.950 (total time: 36.690) Filter (dist only) r_work=0.0976 r_free=0.1834 | n_water=221 | time (s): 17.670 (total time: 54.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.992760 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.196624 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0924 0.1866 0.0942 0.011 1.2 8.6 0.5 0.6 0 0.496 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 18.66 9.42 8.282 18.714 0.197 5.001 9.05 18.54 9.49 8.763 18.793 0.197 4.944 Individual atomic B min max mean iso aniso Overall: 0.00 106.93 17.28 11.50 1748 0 Protein: 0.00 106.93 16.32 11.49 1519 0 Water: 0.00 61.17 23.78 N/A 221 0 Other: 4.70 39.90 19.79 N/A 8 0 Chain A: 0.00 106.93 16.70 N/A 1634 0 Chain S: 0.00 58.01 25.49 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.69 597 10.69 - 21.39 676 21.39 - 32.08 280 32.08 - 42.77 105 42.77 - 53.47 48 53.47 - 64.16 21 64.16 - 74.85 10 74.85 - 85.54 7 85.54 - 96.24 0 96.24 - 106.93 4 =========================== Idealize ADP of riding H ========================== r_work=0.0905 r_free=0.1854 r_work=0.0909 r_free=0.1853 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0909 r_free = 0.1853 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1839 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0903 r_free= 0.1839 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 4.943904 | | target function (ml) not normalized (work): 24338.840020 | | target function (ml) not normalized (free): 2068.183438 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1275 0.1809 5.5066 6.1094| | 2: 3.78 - 3.00 1.00 2430 110 0.0450 0.1889 4.3666 10.915| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.20 1.00 0.94 12289.59| | 2: 3.78 - 3.00 2430 110 0.99 1.97 1.00 0.96 922.73| |alpha: min = 0.93 max = 0.96 mean = 0.95| |beta: min = 594.39 max = 20390.62 mean = 6678.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.90 mean = 7.15| |phase err.(test): min = 0.00 max = 73.92 mean = 7.02| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0950 0.0903 0.1839 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2193 0.2195 0.2260 n_refl.: 5175 remove outliers: r(all,work,free)=0.2193 0.2195 0.2260 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2193 0.2195 0.2260 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0950 0.0903 0.1842 n_refl.: 5175 remove outliers: r(all,work,free)=0.0950 0.0903 0.1842 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3963 314.879 288.523 0.602 0.988 0.319 11.894-9.307 99.02 97 4 0.1904 506.541 492.786 0.998 0.994 0.318 9.237-7.194 100.00 213 7 0.2127 414.250 404.795 1.061 0.998 0.310 7.162-5.571 100.00 427 22 0.2082 310.844 301.895 1.039 0.999 0.290 5.546-4.326 100.00 867 58 0.1037 426.745 421.160 1.069 1.000 0.230 4.315-3.360 100.00 1859 96 0.0578 405.839 405.389 1.147 1.002 0.220 3.356-3.002 100.00 1373 60 0.0435 312.594 312.597 1.137 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.6314 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3617 0.2028 0.081 5.348 8.8 119.3 19.9 258 0.000 1_bss: 0.1563 0.1596 0.081 5.348 6.3 116.8 17.4 258 0.000 1_settarget: 0.1563 0.1596 0.081 5.348 6.3 116.8 17.4 258 0.000 1_nqh: 0.1563 0.1597 0.081 5.348 6.3 116.8 17.4 258 0.003 1_weight: 0.1563 0.1597 0.081 5.348 6.3 116.8 17.4 258 0.003 1_xyzrec: 0.1162 0.1789 0.010 0.993 6.3 116.8 17.4 258 0.204 1_adp: 0.1018 0.1783 0.010 0.993 2.6 111.9 17.8 258 0.204 1_regHadp: 0.1011 0.1787 0.010 0.993 2.6 111.9 17.8 258 0.204 1_occ: 0.1015 0.1774 0.010 0.993 2.6 111.9 17.8 258 0.204 2_bss: 0.1017 0.1782 0.010 0.993 1.6 110.9 16.9 258 0.204 2_settarget: 0.1017 0.1782 0.010 0.993 1.6 110.9 16.9 258 0.204 2_updatecdl: 0.1017 0.1782 0.010 1.013 1.6 110.9 16.9 258 0.204 2_nqh: 0.1017 0.1782 0.010 1.013 1.6 110.9 16.9 258 0.206 2_sol: 0.1129 0.1690 0.010 1.013 1.0 110.9 16.3 229 n/a 2_weight: 0.1129 0.1690 0.010 1.013 1.0 110.9 16.3 229 n/a 2_xyzrec: 0.1016 0.1832 0.010 0.999 1.0 110.9 16.3 229 n/a 2_adp: 0.0950 0.1866 0.010 0.999 0.0 106.9 17.0 229 n/a 2_regHadp: 0.0946 0.1867 0.010 0.999 0.0 106.9 17.0 229 n/a 2_occ: 0.0939 0.1864 0.010 0.999 0.0 106.9 17.0 229 n/a 3_bss: 0.0940 0.1875 0.010 0.999 0.0 106.9 17.0 229 n/a 3_settarget: 0.0940 0.1875 0.010 0.999 0.0 106.9 17.0 229 n/a 3_updatecdl: 0.0940 0.1875 0.010 1.004 0.0 106.9 17.0 229 n/a 3_nqh: 0.0941 0.1879 0.010 1.004 0.0 106.9 17.0 229 n/a 3_sol: 0.1052 0.1830 0.010 1.004 0.0 106.9 16.7 228 n/a 3_weight: 0.1052 0.1830 0.010 1.004 0.0 106.9 16.7 228 n/a 3_xyzrec: 0.0945 0.1884 0.011 1.102 0.0 106.9 16.7 228 n/a 3_adp: 0.0901 0.1878 0.011 1.102 0.0 106.0 16.8 228 n/a 3_regHadp: 0.0906 0.1884 0.011 1.102 0.0 106.0 16.8 228 n/a 3_occ: 0.0893 0.1866 0.011 1.102 0.0 106.0 16.8 228 n/a 4_bss: 0.0887 0.1863 0.011 1.102 0.0 106.0 16.8 228 n/a 4_settarget: 0.0887 0.1863 0.011 1.102 0.0 106.0 16.8 228 n/a 4_updatecdl: 0.0887 0.1863 0.011 1.119 0.0 106.0 16.8 228 n/a 4_nqh: 0.0887 0.1863 0.011 1.119 0.0 106.0 16.8 228 n/a 4_sol: 0.1008 0.1851 0.011 1.119 0.0 106.0 16.8 221 n/a 4_weight: 0.1008 0.1851 0.011 1.119 0.0 106.0 16.8 221 n/a 4_xyzrec: 0.0915 0.1830 0.011 1.074 0.0 106.0 16.8 221 n/a 4_adp: 0.0887 0.1854 0.011 1.074 0.0 105.4 16.9 221 n/a 4_regHadp: 0.0893 0.1859 0.011 1.074 0.0 105.4 16.9 221 n/a 4_occ: 0.0881 0.1835 0.011 1.074 0.0 105.4 16.9 221 n/a 5_bss: 0.0880 0.1835 0.011 1.074 0.0 105.4 16.9 221 n/a 5_settarget: 0.0880 0.1835 0.011 1.074 0.0 105.4 16.9 221 n/a 5_updatecdl: 0.0880 0.1835 0.011 1.080 0.0 105.4 16.9 221 n/a 5_setrh: 0.0883 0.1835 0.011 1.080 0.0 105.4 16.9 221 n/a 5_nqh: 0.0883 0.1832 0.011 1.080 0.0 105.4 16.9 221 n/a 5_sol: 0.0976 0.1834 0.011 1.080 0.0 105.4 17.1 221 n/a 5_weight: 0.0976 0.1834 0.011 1.080 0.0 105.4 17.1 221 n/a 5_xyzrec: 0.0924 0.1866 0.011 1.158 0.0 105.4 17.1 221 n/a 5_adp: 0.0905 0.1854 0.011 1.158 0.0 106.9 17.3 221 n/a 5_regHadp: 0.0909 0.1853 0.011 1.158 0.0 106.9 17.3 221 n/a 5_occ: 0.0903 0.1839 0.011 1.158 0.0 106.9 17.3 221 n/a end: 0.0903 0.1842 0.011 1.158 0.0 106.9 17.3 221 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6318584_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6318584_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4200 Refinement macro-cycles (run) : 481.8400 Write final files (write_after_run_outputs) : 10.8800 Total : 496.1400 Total CPU time: 8.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:57 PST -0800 (1735492737.34 s) Start R-work = 0.1563, R-free = 0.1596 Final R-work = 0.0903, R-free = 0.1842 =============================================================================== Job complete usr+sys time: 523.96 seconds wall clock time: 9 minutes 5.98 seconds (545.98 seconds total)